The Survival Scatter plot shows the clinical status (i.e. dead or alive) for all individuals in the patient cohort, based on the same data that underlies the corresponding Kaplan-Meier plots. Patients that are alive at last time for follow-up are shown in blue and patients who have died during the study are shown in red. The x-axis shows the expression levels (FPKM) of the investigated gene in the tumor tissue at the time of diagnosis. The y-axis shows the follow-up time after diagnosis (years). Both axes are complimented with kernel density curves demonstrating the data density over the axes. The top density plot shows the expression levels (FPKM) distribution among dead (red) and alive patients (blue). The right density plot shows the data density of the survived years of dead patients with high and low expression levels respectively, stratified using the cutoff indicated by the vertical dashed line through the Survival Scatter plot. This cutoff is automatically defined based on the FPKM cutoff that minimizes the p-score. The interactive Survival Scatter plot allows for the cutoff to be changed by dragging the vertical line or by entering a cutoff value in the square labeled "Survival analysis". Under the Survival Scatter plot the p-score landscape is shown together with the difference in median between survival time for patients who have died with respect to high and low expression. This is intended to aid the user in exploring custom cutoffs.

Individual patient data is displayed in an interactive plot and can be filtered by clicking on one or more of the category buttons on the top of the page. Categories describing expression level and patient information include: high, low, alive, dead, female, male and tumor stages. The scale of the x-axis can be toggled between linear and log-scale by clicking on the "x log" button. Mouse-over function shows TCGA ID, patient information and mRNA expression (FPKM) for each patient.

& Survival analysisi

Kaplan-Meier plots summarize results from analysis of correlation between mRNA expression level and patient survival. Patients were divided based on level of expression into one of the two groups "low" (under cut off) or "high" (over cut off).

Based on the FPKM value of each gene, we classified the patients into two groups and examined their prognoses. In the analysis, we excluded genes with low expression, i.e., those with a median expression among samples less than FPKM 1. The prognosis of each group of patients was examined by Kaplan-Meier survival estimators, and the survival outcomes of the two groups were compared by log-rank tests. To choose the best FPKM cut-offs for grouping the patients most significantly, all FPKM values from the 20th to 80th percentiles were used to group the patients, significant differences in the survival outcomes of the groups were examined and the value yielding the lowest log-rank P value is selected.

5-year survival for patients with higher expression than the expression cutoff.

For melanoma and glioma, 3-year survival is shown.

N/A5-year survival lowi

5-year survival for patients with lower expression than the expression cutoff.

For melanoma and glioma, 3-year survival is shown.

N/A

TCGA RNA samplesi

RNA-seq data is reported as median FPKM (number Fragments Per Kilobase of exon per Million reads), generated by the The Cancer Genome Atlas (TCGA) .

Normal distribution across the dataset is visualized with box plots, shown as median and 25th and 75th percentiles. Points are displayed as outliers if they are above or below 1.5 times the interquartile range. FPKM values of the individual samples are presented next to the box plot.

Average FPKM

5.3

Number of samples

597

Samples

Sample

Description

FPKM

TCGA-AA-3561-01A

72 years, male, stage:iia, alive, 424 days

22.1

TCGA-A6-6648-01A

56 years, male, white, stage:iva, alive, 766 days

11.4

TCGA-AA-3697-01A

77 years, male, stage:ii, alive, 2587 days

9.6

TCGA-D5-6922-01A

76 years, male, white, stage:iiia, alive, 308 days

9.5

TCGA-A6-2672-01B

82 years, female, white, stage:iiib, alive, 1419 days

9.3

TCGA-DM-A28H-01A

50 years, male, white, stage:iiic, alive, 3561 days

9.2

TCGA-CK-5914-01A

81 years, male, white, stage:iiib, alive, 669 days

9.2

TCGA-D5-6539-01A

45 years, female, white, alive, 380 days

9.2

TCGA-AF-2693-01A

75 years, male, white, stage:i, alive, 1155 days

9.1

TCGA-EI-6511-01A

52 years, male, white, stage:iiib, alive, 482 days

9.0

TCGA-AA-3560-01A

72 years, female, stage:iiic, alive, 608 days

8.8

TCGA-AG-3582-01A

75 years, male, stage:iv, dead, 1096 days

8.7

TCGA-DM-A28K-01A

75 years, male, white, stage:iia, alive, 2988 days

8.7

TCGA-G4-6626-01A

90 years, male, white, stage:iia, dead, 1422 days

8.6

TCGA-G4-6295-01A

70 years, female, white, stage:ii, alive, 254 days

8.6

TCGA-AA-A02F-01A

68 years, female, stage:iv, alive, 1216 days

8.3

TCGA-A6-6138-01A

61 years, male, white, stage:i, alive, 685 days

8.1

TCGA-D5-6926-01A

65 years, male, white, stage:iiib, alive, 275 days

8.0

TCGA-AF-6136-01A

72 years, female, white, stage:iiib, alive, 741 days

8.0

TCGA-DM-A288-01A

68 years, male, white, stage:iiic, dead, 427 days

8.0

TCGA-AA-3673-01A

53 years, female, stage:ii, alive, 1522 days

8.0

TCGA-AA-3552-01A

85 years, male, stage:iiic, dead, 396 days

8.0

TCGA-EI-6881-01A

60 years, male, white, stage:iiia, alive, 499 days

8.0

TCGA-CK-5912-01A

82 years, male, white, stage:i, dead, 1493 days

8.0

TCGA-AZ-4682-01B

61 years, male, white, stage:iva, dead, 680 days

7.9

TCGA-DM-A1DA-01A

71 years, female, white, stage:iiic, dead, 228 days

7.8

TCGA-AG-3578-01A

76 years, female, stage:iia, alive, 974 days

7.8

TCGA-AA-A01D-01A

47 years, female, stage:iiic, dead, 334 days

7.8

TCGA-F4-6704-01A

60 years, male, american indian or alaska native, stage:iiic, alive, 47 days

A mouse-over function shows sample information and annotation data. Click on an image to view it in a full screen mode. Samples can be filtered based on level of antibody staining by selecting one or several of the following categories: high, medium, low and not detected. The assay and annotation is described here.

Note that samples used for immunohistochemistry by the Human Protein Atlas do not correspond to samples in the TCGA dataset.

Antibody stainingi

Kaplan-Meier plots summarize results from analysis of correlation between mRNA expression level and patient survival. Patients were divided based on level of expression into one of the two groups "low" (under cut off) or "high" (over cut off).